Starting phenix.real_space_refine on Fri Feb 16 10:30:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsj_22456/02_2024/7jsj_22456_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsj_22456/02_2024/7jsj_22456.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsj_22456/02_2024/7jsj_22456_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsj_22456/02_2024/7jsj_22456_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsj_22456/02_2024/7jsj_22456_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsj_22456/02_2024/7jsj_22456.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsj_22456/02_2024/7jsj_22456.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsj_22456/02_2024/7jsj_22456_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsj_22456/02_2024/7jsj_22456_trim_updated.pdb" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 16 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 64 5.16 5 Na 4 4.78 5 C 4940 2.51 5 N 1152 2.21 5 O 1228 1.98 5 H 7668 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 307": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 307": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15056 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 7491 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 29, 'TRANS': 438} Chain breaks: 4 Chain: "B" Number of atoms: 7491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 7491 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 29, 'TRANS': 438} Chain breaks: 4 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 37 Unusual residues: {' NA': 2, 'NAG': 1, 'X3M': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 37 Unusual residues: {' NA': 2, 'NAG': 1, 'X3M': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.91, per 1000 atoms: 0.46 Number of scatterers: 15056 At special positions: 0 Unit cell: (85.84, 82.621, 108.373, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 64 16.00 Na 4 11.00 O 1228 8.00 N 1152 7.00 C 4940 6.00 H 7668 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 562 " " NAG B 601 " - " ASN B 562 " Time building additional restraints: 12.11 Conformation dependent library (CDL) restraints added in 1.3 seconds 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1780 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 0 sheets defined 71.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'A' and resid 16 through 18 No H-bonds generated for 'chain 'A' and resid 16 through 18' Processing helix chain 'A' and resid 21 through 27 Proline residue: A 26 - end of helix Processing helix chain 'A' and resid 34 through 50 Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 63 through 66 No H-bonds generated for 'chain 'A' and resid 63 through 66' Processing helix chain 'A' and resid 76 through 81 removed outlier: 4.728A pdb=" N GLN A 81 " --> pdb=" O GLN A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 102 Processing helix chain 'A' and resid 106 through 117 removed outlier: 3.697A pdb=" N LEU A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 136 removed outlier: 3.543A pdb=" N LEU A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 157 Proline residue: A 150 - end of helix Processing helix chain 'A' and resid 203 through 221 removed outlier: 3.737A pdb=" N CYS A 213 " --> pdb=" O THR A 209 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N THR A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 240 Processing helix chain 'A' and resid 250 through 275 Proline residue: A 259 - end of helix Processing helix chain 'A' and resid 293 through 296 No H-bonds generated for 'chain 'A' and resid 293 through 296' Processing helix chain 'A' and resid 299 through 309 removed outlier: 3.937A pdb=" N GLU A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS A 308 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 332 removed outlier: 3.513A pdb=" N ASN A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 368 removed outlier: 3.949A pdb=" N PHE A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 404 Processing helix chain 'A' and resid 409 through 427 removed outlier: 3.968A pdb=" N LEU A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY A 415 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 435 Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 445 through 461 removed outlier: 3.908A pdb=" N GLU A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 483 removed outlier: 3.912A pdb=" N THR A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) Proline residue: A 474 - end of helix removed outlier: 3.626A pdb=" N SER A 482 " --> pdb=" O SER A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 499 removed outlier: 4.563A pdb=" N LEU A 492 " --> pdb=" O TYR A 489 " (cutoff:3.500A) Proline residue: A 493 - end of helix removed outlier: 3.634A pdb=" N ALA A 498 " --> pdb=" O THR A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 507 No H-bonds generated for 'chain 'A' and resid 505 through 507' Processing helix chain 'A' and resid 509 through 517 removed outlier: 4.077A pdb=" N TYR A 517 " --> pdb=" O ILE A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 546 removed outlier: 4.425A pdb=" N ILE A 531 " --> pdb=" O LYS A 527 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N MET A 532 " --> pdb=" O THR A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 552 removed outlier: 3.779A pdb=" N PHE A 552 " --> pdb=" O GLY A 548 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 548 through 552' Processing helix chain 'B' and resid 16 through 18 No H-bonds generated for 'chain 'B' and resid 16 through 18' Processing helix chain 'B' and resid 21 through 27 Proline residue: B 26 - end of helix Processing helix chain 'B' and resid 34 through 50 Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 63 through 66 No H-bonds generated for 'chain 'B' and resid 63 through 66' Processing helix chain 'B' and resid 76 through 81 removed outlier: 4.729A pdb=" N GLN B 81 " --> pdb=" O GLN B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 102 Processing helix chain 'B' and resid 106 through 117 removed outlier: 3.698A pdb=" N LEU B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 136 removed outlier: 3.544A pdb=" N LEU B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 157 Proline residue: B 150 - end of helix Processing helix chain 'B' and resid 203 through 221 removed outlier: 3.738A pdb=" N CYS B 213 " --> pdb=" O THR B 209 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N THR B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 240 Processing helix chain 'B' and resid 250 through 275 Proline residue: B 259 - end of helix Processing helix chain 'B' and resid 293 through 296 No H-bonds generated for 'chain 'B' and resid 293 through 296' Processing helix chain 'B' and resid 299 through 309 removed outlier: 3.937A pdb=" N GLU B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS B 308 " --> pdb=" O GLU B 304 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 332 Processing helix chain 'B' and resid 356 through 368 removed outlier: 3.949A pdb=" N PHE B 368 " --> pdb=" O ALA B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 404 Processing helix chain 'B' and resid 408 through 427 removed outlier: 4.212A pdb=" N LEU B 413 " --> pdb=" O ILE B 410 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU B 414 " --> pdb=" O VAL B 411 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER B 427 " --> pdb=" O SER B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 435 Processing helix chain 'B' and resid 439 through 441 No H-bonds generated for 'chain 'B' and resid 439 through 441' Processing helix chain 'B' and resid 445 through 461 removed outlier: 3.908A pdb=" N GLU B 461 " --> pdb=" O ALA B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 483 removed outlier: 3.912A pdb=" N THR B 469 " --> pdb=" O ASN B 465 " (cutoff:3.500A) Proline residue: B 474 - end of helix removed outlier: 3.625A pdb=" N SER B 482 " --> pdb=" O SER B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 499 removed outlier: 4.564A pdb=" N LEU B 492 " --> pdb=" O TYR B 489 " (cutoff:3.500A) Proline residue: B 493 - end of helix removed outlier: 3.634A pdb=" N ALA B 498 " --> pdb=" O THR B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 507 No H-bonds generated for 'chain 'B' and resid 505 through 507' Processing helix chain 'B' and resid 509 through 517 removed outlier: 4.078A pdb=" N TYR B 517 " --> pdb=" O ILE B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 546 removed outlier: 4.424A pdb=" N ILE B 531 " --> pdb=" O LYS B 527 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET B 532 " --> pdb=" O THR B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 552 removed outlier: 3.779A pdb=" N PHE B 552 " --> pdb=" O GLY B 548 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 548 through 552' 385 hydrogen bonds defined for protein. 1071 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.16 Time building geometry restraints manager: 12.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7648 1.03 - 1.22: 22 1.22 - 1.42: 3016 1.42 - 1.61: 4450 1.61 - 1.81: 108 Bond restraints: 15244 Sorted by residual: bond pdb=" C1 NAG B 601 " pdb=" C2 NAG B 601 " ideal model delta sigma weight residual 1.532 1.599 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C1 NAG A 601 " pdb=" C2 NAG A 601 " ideal model delta sigma weight residual 1.532 1.598 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" C7 NAG A 601 " pdb=" N2 NAG A 601 " ideal model delta sigma weight residual 1.346 1.393 -0.047 2.00e-02 2.50e+03 5.50e+00 bond pdb=" C7 NAG B 601 " pdb=" N2 NAG B 601 " ideal model delta sigma weight residual 1.346 1.393 -0.047 2.00e-02 2.50e+03 5.43e+00 bond pdb=" C02 X3M A 602 " pdb=" C05 X3M A 602 " ideal model delta sigma weight residual 1.530 1.487 0.043 2.00e-02 2.50e+03 4.66e+00 ... (remaining 15239 not shown) Histogram of bond angle deviations from ideal: 72.69 - 85.79: 162 85.79 - 98.89: 4 98.89 - 111.99: 17957 111.99 - 125.09: 9106 125.09 - 138.19: 519 Bond angle restraints: 27748 Sorted by residual: angle pdb=" CB VAL A 263 " pdb=" CA VAL A 263 " pdb=" HA VAL A 263 " ideal model delta sigma weight residual 109.00 72.69 36.31 3.00e+00 1.11e-01 1.46e+02 angle pdb=" CB VAL B 263 " pdb=" CA VAL B 263 " pdb=" HA VAL B 263 " ideal model delta sigma weight residual 109.00 72.86 36.14 3.00e+00 1.11e-01 1.45e+02 angle pdb=" C SER B 291 " pdb=" CA SER B 291 " pdb=" HA SER B 291 " ideal model delta sigma weight residual 109.00 73.34 35.66 3.00e+00 1.11e-01 1.41e+02 angle pdb=" C SER A 291 " pdb=" CA SER A 291 " pdb=" HA SER A 291 " ideal model delta sigma weight residual 109.00 73.62 35.38 3.00e+00 1.11e-01 1.39e+02 angle pdb=" N SER A 291 " pdb=" CA SER A 291 " pdb=" HA SER A 291 " ideal model delta sigma weight residual 110.00 74.85 35.15 3.00e+00 1.11e-01 1.37e+02 ... (remaining 27743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.73: 6805 25.73 - 51.46: 300 51.46 - 77.20: 71 77.20 - 102.93: 4 102.93 - 128.66: 4 Dihedral angle restraints: 7184 sinusoidal: 3880 harmonic: 3304 Sorted by residual: dihedral pdb=" CA THR B 225 " pdb=" C THR B 225 " pdb=" N GLY B 226 " pdb=" CA GLY B 226 " ideal model delta harmonic sigma weight residual 180.00 152.59 27.41 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA THR A 225 " pdb=" C THR A 225 " pdb=" N GLY A 226 " pdb=" CA GLY A 226 " ideal model delta harmonic sigma weight residual 180.00 152.60 27.40 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA TYR A 353 " pdb=" C TYR A 353 " pdb=" N VAL A 354 " pdb=" CA VAL A 354 " ideal model delta harmonic sigma weight residual -180.00 -154.73 -25.27 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 7181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.345: 1232 0.345 - 0.689: 2 0.689 - 1.034: 0 1.034 - 1.378: 4 1.378 - 1.723: 12 Chirality restraints: 1250 Sorted by residual: chirality pdb=" CG LEU B 27 " pdb=" CB LEU B 27 " pdb=" CD1 LEU B 27 " pdb=" CD2 LEU B 27 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.72 2.00e-01 2.50e+01 7.42e+01 chirality pdb=" CG LEU A 27 " pdb=" CB LEU A 27 " pdb=" CD1 LEU A 27 " pdb=" CD2 LEU A 27 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.72 2.00e-01 2.50e+01 7.36e+01 chirality pdb=" CG LEU A 23 " pdb=" CB LEU A 23 " pdb=" CD1 LEU A 23 " pdb=" CD2 LEU A 23 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.10e+01 ... (remaining 1247 not shown) Planarity restraints: 2106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 406 " -0.031 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO B 407 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 407 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 407 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 406 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO A 407 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 407 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 407 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 310 " -0.029 5.00e-02 4.00e+02 4.45e-02 3.16e+00 pdb=" N PRO A 311 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 311 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 311 " -0.025 5.00e-02 4.00e+02 ... (remaining 2103 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.13: 642 2.13 - 2.75: 28254 2.75 - 3.37: 42832 3.37 - 3.98: 54204 3.98 - 4.60: 88980 Nonbonded interactions: 214912 Sorted by model distance: nonbonded pdb=" O LYS A 120 " pdb=" H LEU A 124 " model vdw 1.516 1.850 nonbonded pdb=" O LYS B 120 " pdb=" H LEU B 124 " model vdw 1.516 1.850 nonbonded pdb=" O THR B 225 " pdb=" H THR B 227 " model vdw 1.553 1.850 nonbonded pdb=" O THR A 225 " pdb=" H THR A 227 " model vdw 1.554 1.850 nonbonded pdb=" O MET A 31 " pdb=" H ALA A 33 " model vdw 1.558 1.850 ... (remaining 214907 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.230 Extract box with map and model: 6.340 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 50.040 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 7576 Z= 0.510 Angle : 1.118 26.291 10336 Z= 0.488 Chirality : 0.182 1.723 1250 Planarity : 0.005 0.046 1236 Dihedral : 13.617 128.662 2704 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.17 % Favored : 90.61 % Rotamer: Outliers : 7.23 % Allowed : 8.73 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.30), residues: 916 helix: 0.84 (0.21), residues: 682 sheet: None (None), residues: 0 loop : -3.23 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 560 HIS 0.002 0.000 HIS A 519 PHE 0.019 0.001 PHE A 35 TYR 0.012 0.001 TYR A 353 ARG 0.002 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 102 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.6705 (mmt) REVERT: A 240 LEU cc_start: 0.8040 (mt) cc_final: 0.7616 (mt) REVERT: A 312 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6461 (tt) REVERT: A 391 PHE cc_start: 0.4442 (OUTLIER) cc_final: 0.3827 (m-80) REVERT: A 392 TYR cc_start: 0.6859 (OUTLIER) cc_final: 0.5332 (m-80) REVERT: A 458 VAL cc_start: 0.8314 (t) cc_final: 0.8111 (m) REVERT: B 115 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7978 (mt) REVERT: B 158 GLN cc_start: 0.6871 (OUTLIER) cc_final: 0.6322 (mm-40) REVERT: B 312 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7166 (tt) REVERT: B 369 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7897 (pt) REVERT: B 391 PHE cc_start: 0.4144 (OUTLIER) cc_final: 0.3228 (t80) REVERT: B 392 TYR cc_start: 0.3641 (OUTLIER) cc_final: 0.2582 (m-80) outliers start: 58 outliers final: 18 residues processed: 154 average time/residue: 0.4129 time to fit residues: 86.0560 Evaluate side-chains 109 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 81 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 106 HIS Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 106 HIS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 0.0670 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 43 optimal weight: 0.2980 chunk 53 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 545 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7576 Z= 0.207 Angle : 1.058 26.663 10336 Z= 0.464 Chirality : 0.181 1.737 1250 Planarity : 0.005 0.044 1236 Dihedral : 11.225 106.896 1087 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.97 % Favored : 91.81 % Rotamer: Outliers : 4.24 % Allowed : 11.72 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.30), residues: 916 helix: 1.12 (0.21), residues: 674 sheet: None (None), residues: 0 loop : -2.86 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 49 HIS 0.006 0.001 HIS A 441 PHE 0.018 0.001 PHE B 258 TYR 0.009 0.001 TYR B 353 ARG 0.003 0.000 ARG B 481 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 88 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.6671 (mmt) REVERT: A 312 LEU cc_start: 0.6931 (OUTLIER) cc_final: 0.6322 (tt) REVERT: A 391 PHE cc_start: 0.4686 (OUTLIER) cc_final: 0.4110 (m-80) REVERT: A 392 TYR cc_start: 0.6849 (OUTLIER) cc_final: 0.5316 (m-80) REVERT: B 115 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8018 (mt) REVERT: B 158 GLN cc_start: 0.6832 (OUTLIER) cc_final: 0.6194 (mm-40) REVERT: B 312 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7246 (tt) REVERT: B 391 PHE cc_start: 0.4179 (OUTLIER) cc_final: 0.3276 (t80) REVERT: B 392 TYR cc_start: 0.4036 (OUTLIER) cc_final: 0.3007 (m-80) outliers start: 34 outliers final: 21 residues processed: 116 average time/residue: 0.3418 time to fit residues: 57.4682 Evaluate side-chains 114 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 84 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 106 HIS Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 106 HIS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 0.0770 chunk 25 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7576 Z= 0.239 Angle : 1.041 26.226 10336 Z= 0.456 Chirality : 0.182 1.727 1250 Planarity : 0.005 0.046 1236 Dihedral : 10.690 90.316 1077 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.30 % Favored : 91.48 % Rotamer: Outliers : 4.49 % Allowed : 12.72 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.30), residues: 916 helix: 1.20 (0.21), residues: 672 sheet: None (None), residues: 0 loop : -2.73 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 49 HIS 0.007 0.001 HIS A 556 PHE 0.014 0.001 PHE B 258 TYR 0.010 0.001 TYR B 353 ARG 0.001 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 113 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.6805 (mmt) REVERT: A 312 LEU cc_start: 0.6979 (OUTLIER) cc_final: 0.6340 (tt) REVERT: A 391 PHE cc_start: 0.4820 (OUTLIER) cc_final: 0.4056 (m-80) REVERT: A 392 TYR cc_start: 0.6842 (OUTLIER) cc_final: 0.5260 (m-80) REVERT: B 115 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8051 (mt) REVERT: B 158 GLN cc_start: 0.6906 (OUTLIER) cc_final: 0.6225 (mm-40) REVERT: B 312 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7228 (tt) REVERT: B 369 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7905 (pt) REVERT: B 391 PHE cc_start: 0.4274 (OUTLIER) cc_final: 0.3332 (t80) REVERT: B 392 TYR cc_start: 0.3960 (OUTLIER) cc_final: 0.2942 (m-80) outliers start: 36 outliers final: 24 residues processed: 139 average time/residue: 0.3544 time to fit residues: 70.7003 Evaluate side-chains 133 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 99 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 106 HIS Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 106 HIS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7576 Z= 0.261 Angle : 1.048 26.275 10336 Z= 0.459 Chirality : 0.182 1.730 1250 Planarity : 0.005 0.042 1236 Dihedral : 10.104 86.938 1075 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.62 % Favored : 91.16 % Rotamer: Outliers : 4.86 % Allowed : 13.59 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.30), residues: 916 helix: 1.25 (0.21), residues: 666 sheet: None (None), residues: 0 loop : -2.58 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 49 HIS 0.007 0.001 HIS A 556 PHE 0.014 0.001 PHE A 35 TYR 0.010 0.001 TYR B 353 ARG 0.002 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 105 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.6706 (mmt) REVERT: A 304 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6201 (mp0) REVERT: A 312 LEU cc_start: 0.6982 (OUTLIER) cc_final: 0.6289 (tt) REVERT: A 391 PHE cc_start: 0.4859 (OUTLIER) cc_final: 0.4032 (m-80) REVERT: A 392 TYR cc_start: 0.6871 (OUTLIER) cc_final: 0.5290 (m-80) REVERT: B 51 THR cc_start: 0.7669 (OUTLIER) cc_final: 0.7464 (t) REVERT: B 115 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8188 (mt) REVERT: B 158 GLN cc_start: 0.6979 (OUTLIER) cc_final: 0.6326 (mm-40) REVERT: B 369 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.7943 (pt) REVERT: B 391 PHE cc_start: 0.4533 (OUTLIER) cc_final: 0.3496 (t80) REVERT: B 392 TYR cc_start: 0.3831 (OUTLIER) cc_final: 0.2802 (m-80) REVERT: B 517 TYR cc_start: 0.8370 (m-80) cc_final: 0.8120 (m-80) outliers start: 39 outliers final: 24 residues processed: 133 average time/residue: 0.3206 time to fit residues: 63.6349 Evaluate side-chains 134 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 99 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 106 HIS Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 106 HIS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 0.0870 chunk 1 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN B 465 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7576 Z= 0.228 Angle : 1.034 26.211 10336 Z= 0.450 Chirality : 0.182 1.730 1250 Planarity : 0.005 0.044 1236 Dihedral : 9.619 87.827 1072 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.30 % Favored : 91.38 % Rotamer: Outliers : 4.49 % Allowed : 14.21 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.30), residues: 916 helix: 1.40 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -2.49 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 49 HIS 0.006 0.001 HIS A 441 PHE 0.012 0.001 PHE A 35 TYR 0.009 0.001 TYR B 353 ARG 0.002 0.000 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 99 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 304 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6225 (mp0) REVERT: A 312 LEU cc_start: 0.6930 (OUTLIER) cc_final: 0.6244 (tt) REVERT: A 391 PHE cc_start: 0.4893 (OUTLIER) cc_final: 0.3995 (m-80) REVERT: A 392 TYR cc_start: 0.6843 (OUTLIER) cc_final: 0.5277 (m-80) REVERT: B 51 THR cc_start: 0.7696 (OUTLIER) cc_final: 0.7496 (t) REVERT: B 115 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8234 (mt) REVERT: B 158 GLN cc_start: 0.6974 (OUTLIER) cc_final: 0.6767 (mm-40) REVERT: B 391 PHE cc_start: 0.4487 (OUTLIER) cc_final: 0.3348 (t80) REVERT: B 392 TYR cc_start: 0.3928 (OUTLIER) cc_final: 0.2925 (m-80) REVERT: B 517 TYR cc_start: 0.8368 (m-80) cc_final: 0.8127 (m-80) outliers start: 36 outliers final: 24 residues processed: 127 average time/residue: 0.3215 time to fit residues: 60.3836 Evaluate side-chains 130 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 97 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 106 HIS Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 106 HIS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 41 optimal weight: 0.1980 chunk 7 optimal weight: 0.9980 chunk 29 optimal weight: 0.3980 chunk 46 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN A 545 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7576 Z= 0.228 Angle : 1.033 26.234 10336 Z= 0.447 Chirality : 0.182 1.728 1250 Planarity : 0.005 0.041 1236 Dihedral : 9.092 88.922 1068 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.97 % Favored : 91.70 % Rotamer: Outliers : 4.61 % Allowed : 14.71 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.30), residues: 916 helix: 1.45 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -2.45 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 49 HIS 0.006 0.001 HIS A 441 PHE 0.012 0.001 PHE A 35 TYR 0.010 0.001 TYR B 353 ARG 0.002 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 98 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 304 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6229 (mp0) REVERT: A 312 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.6346 (tt) REVERT: A 391 PHE cc_start: 0.4900 (OUTLIER) cc_final: 0.3947 (m-80) REVERT: A 392 TYR cc_start: 0.6900 (OUTLIER) cc_final: 0.5278 (m-80) REVERT: B 51 THR cc_start: 0.7717 (OUTLIER) cc_final: 0.7509 (t) REVERT: B 115 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8210 (mt) REVERT: B 158 GLN cc_start: 0.6848 (OUTLIER) cc_final: 0.6637 (mm-40) REVERT: B 391 PHE cc_start: 0.4487 (OUTLIER) cc_final: 0.3391 (t80) REVERT: B 392 TYR cc_start: 0.4127 (OUTLIER) cc_final: 0.3153 (m-80) REVERT: B 517 TYR cc_start: 0.8375 (m-80) cc_final: 0.8159 (m-80) outliers start: 37 outliers final: 25 residues processed: 127 average time/residue: 0.3395 time to fit residues: 65.0267 Evaluate side-chains 130 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 96 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 106 HIS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 559 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN A 545 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7576 Z= 0.272 Angle : 1.038 26.246 10336 Z= 0.453 Chirality : 0.182 1.727 1250 Planarity : 0.005 0.038 1236 Dihedral : 8.895 88.599 1064 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.95 % Favored : 90.72 % Rotamer: Outliers : 4.61 % Allowed : 15.09 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.30), residues: 916 helix: 1.37 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -2.50 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 49 HIS 0.006 0.001 HIS A 441 PHE 0.013 0.001 PHE A 35 TYR 0.009 0.001 TYR B 353 ARG 0.003 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 101 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 MET cc_start: 0.6750 (mmm) cc_final: 0.6484 (mmt) REVERT: A 304 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6383 (mp0) REVERT: A 391 PHE cc_start: 0.4943 (OUTLIER) cc_final: 0.3935 (m-80) REVERT: A 392 TYR cc_start: 0.6928 (OUTLIER) cc_final: 0.5273 (m-80) REVERT: B 158 GLN cc_start: 0.7038 (OUTLIER) cc_final: 0.6720 (mm-40) REVERT: B 391 PHE cc_start: 0.4567 (OUTLIER) cc_final: 0.3582 (t80) REVERT: B 392 TYR cc_start: 0.4116 (OUTLIER) cc_final: 0.3170 (m-80) outliers start: 37 outliers final: 26 residues processed: 132 average time/residue: 0.3653 time to fit residues: 68.6807 Evaluate side-chains 127 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 95 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 106 HIS Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 106 HIS Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 60 optimal weight: 0.1980 chunk 43 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7576 Z= 0.216 Angle : 1.026 26.190 10336 Z= 0.445 Chirality : 0.182 1.729 1250 Planarity : 0.005 0.065 1236 Dihedral : 8.528 89.133 1060 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.86 % Favored : 91.81 % Rotamer: Outliers : 4.24 % Allowed : 15.09 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.30), residues: 916 helix: 1.50 (0.21), residues: 658 sheet: None (None), residues: 0 loop : -2.45 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 49 HIS 0.006 0.001 HIS A 441 PHE 0.012 0.001 PHE B 314 TYR 0.009 0.001 TYR B 353 ARG 0.010 0.000 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 99 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 MET cc_start: 0.6703 (mmm) cc_final: 0.6486 (mmt) REVERT: A 304 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.6364 (mp0) REVERT: A 391 PHE cc_start: 0.4939 (OUTLIER) cc_final: 0.3858 (m-80) REVERT: A 392 TYR cc_start: 0.6901 (OUTLIER) cc_final: 0.5257 (m-80) REVERT: B 392 TYR cc_start: 0.4104 (OUTLIER) cc_final: 0.3075 (m-80) outliers start: 34 outliers final: 25 residues processed: 127 average time/residue: 0.3274 time to fit residues: 61.8734 Evaluate side-chains 126 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 97 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 106 HIS Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 35 optimal weight: 0.2980 chunk 64 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 87 optimal weight: 0.0470 chunk 53 optimal weight: 0.8980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7576 Z= 0.215 Angle : 1.024 26.205 10336 Z= 0.443 Chirality : 0.182 1.724 1250 Planarity : 0.005 0.049 1236 Dihedral : 7.893 87.759 1052 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.30 % Favored : 91.48 % Rotamer: Outliers : 3.62 % Allowed : 15.46 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.30), residues: 916 helix: 1.52 (0.22), residues: 654 sheet: None (None), residues: 0 loop : -2.44 (0.41), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 49 HIS 0.005 0.001 HIS A 441 PHE 0.012 0.001 PHE A 35 TYR 0.009 0.001 TYR B 353 ARG 0.008 0.000 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 97 time to evaluate : 1.247 Fit side-chains revert: symmetry clash REVERT: A 304 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6358 (mp0) REVERT: A 391 PHE cc_start: 0.4910 (OUTLIER) cc_final: 0.3837 (m-80) REVERT: A 392 TYR cc_start: 0.6883 (OUTLIER) cc_final: 0.5250 (m-80) REVERT: B 392 TYR cc_start: 0.4064 (OUTLIER) cc_final: 0.3018 (m-80) outliers start: 29 outliers final: 24 residues processed: 122 average time/residue: 0.3140 time to fit residues: 56.7806 Evaluate side-chains 124 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 96 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 106 HIS Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.0670 chunk 60 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7576 Z= 0.236 Angle : 1.030 26.184 10336 Z= 0.447 Chirality : 0.182 1.724 1250 Planarity : 0.005 0.048 1236 Dihedral : 7.791 87.404 1052 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.19 % Favored : 91.59 % Rotamer: Outliers : 3.49 % Allowed : 15.84 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.30), residues: 916 helix: 1.48 (0.22), residues: 654 sheet: None (None), residues: 0 loop : -2.48 (0.41), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 49 HIS 0.006 0.001 HIS A 441 PHE 0.012 0.001 PHE A 35 TYR 0.009 0.001 TYR B 353 ARG 0.008 0.000 ARG B 108 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 102 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 304 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6323 (mp0) REVERT: A 391 PHE cc_start: 0.4856 (OUTLIER) cc_final: 0.3811 (m-80) REVERT: A 392 TYR cc_start: 0.6889 (OUTLIER) cc_final: 0.5254 (m-80) REVERT: B 392 TYR cc_start: 0.3980 (OUTLIER) cc_final: 0.2911 (m-80) outliers start: 28 outliers final: 24 residues processed: 125 average time/residue: 0.3243 time to fit residues: 60.2306 Evaluate side-chains 127 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 99 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 106 HIS Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 75 optimal weight: 0.0980 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 0.1980 chunk 64 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.145464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.132963 restraints weight = 24183.407| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.53 r_work: 0.3553 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7576 Z= 0.218 Angle : 1.025 26.191 10336 Z= 0.444 Chirality : 0.182 1.721 1250 Planarity : 0.005 0.045 1236 Dihedral : 7.714 86.867 1052 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.19 % Favored : 91.48 % Rotamer: Outliers : 3.87 % Allowed : 15.34 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.30), residues: 916 helix: 1.56 (0.22), residues: 654 sheet: None (None), residues: 0 loop : -2.42 (0.41), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 49 HIS 0.005 0.001 HIS A 441 PHE 0.012 0.001 PHE A 35 TYR 0.009 0.001 TYR B 353 ARG 0.007 0.000 ARG B 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3678.73 seconds wall clock time: 65 minutes 38.03 seconds (3938.03 seconds total)